I can do body squats fine (lots of popping, though). I've worked up in weight (though not quite from empty). One week I'll be able to do semi-heavy squats (not even my bodyweight) with no problems and then the next two weeks I can't even add much more than the bar before the knife-in-the-knee. Both knees have the issue, and not simultaneously. The physical therapist says I'm a bit pronated, so I try to account for that in my posture. I tried all the stretches and exercises I was given. It's not like I'm doing things that my legs aren't used to. I'd been doing leg exercises, including squats for a long time. It's just that when I get to about 85-90% of my bodyweight on squats, it'll only be a week or two of no problems and then for the next two weeks I won't be able to do anything.
I do deadlifts, and they usually go just fine except when I've messed up my knees with squats, in which case then my knees will die during deadlifts too. Every time I tell myself I can get back into squats gradually I come back demoralized, and it poisons my other workouts too.
Can you do lunges, band work, step ups/downs, etc... without pain? How are your DLs, core work and glutes? The problem with the knee is that all sorts of other imbalances can show up as knee pain. Also, see if you can find a PT that specializes in sports.
I do deadlifts, and they usually go just fine except when I've messed up my knees with squats, in which case then my knees will die during deadlifts too. Every time I tell myself I can get back into squats gradually I come back demoralized, and it poisons my other workouts too.